RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0136593923:

Variant ID: vg0136593923 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 36593923
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.95, G: 0.05, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

AATAAAGCCCTATTATTGACCTCTAAGCGTGCCATTAGATAGATCTCGAGATTTGAGGAATTTTAGAAGTTGAACGGAGTCAAACGGACTTACGGTTGAG[A/G]
AGATATTGAATTTATAAGATTATTGGATTTTTGGTCTAAAGGAAAAGGATTTATTTAAATCCTTTTTGGAAAAGAAAAGAAAAGAAAAGAAGAAGGGAGG

Reverse complement sequence

CCTCCCTTCTTCTTTTCTTTTCTTTTCTTTTCCAAAAAGGATTTAAATAAATCCTTTTCCTTTAGACCAAAAATCCAATAATCTTATAAATTCAATATCT[T/C]
CTCAACCGTAAGTCCGTTTGACTCCGTTCAACTTCTAAAATTCCTCAAATCTCGAGATCTATCTAATGGCACGCTTAGAGGTCAATAATAGGGCTTTATT

Allele Frequencies:

Search:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	52.00%	47.90%	0.11%	0.00%	NA
All Indica	2759	19.50%	80.30%	0.18%	0.00%	NA
All Japonica	1512	98.60%	1.40%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	32.60%	67.10%	0.34%	0.00%	NA
Indica II	465	4.30%	95.70%	0.00%	0.00%	NA
Indica III	913	17.20%	82.70%	0.11%	0.00%	NA
Indica Intermediate	786	21.40%	78.40%	0.25%	0.00%	NA
Temperate Japonica	767	99.30%	0.70%	0.00%	0.00%	NA
Tropical Japonica	504	97.80%	2.20%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	2.10%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	72.20%	27.80%	0.00%	0.00%	NA

Showing 1 to 13 of 13 entries

Allele Effect:

Search:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0136593923	A -> G	LOC_Os01g63150.1	intron_variant ; MODIFIER	silent_mutation	Average:39.127; most accessible tissue: Zhenshan97 flag leaf, score: 64.768	N	N	N	N

Showing 1 to 1 of 1 entries

Putative Genotype-Phenotype Associations:

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Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0136593923	1.44E-07	NA	mr1517	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0136593923	1.29E-06	1.38E-08	mr1517	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0136593923	2.40E-07	NA	mr1538	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0136593923	5.75E-06	4.63E-06	mr1538	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0136593923	NA	6.61E-10	mr1720	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0136593923	8.60E-06	NA	mr1517_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0136593923	NA	2.99E-07	mr1527_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0136593923	9.59E-08	NA	mr1538_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0136593923	3.85E-06	2.87E-07	mr1538_2	Ind_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251

Showing 1 to 9 of 9 entries

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Search for Variation information by Variation ID:

Detailed information for vg0136593923:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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